Migraines: Cheese and chocolate have been cited as a cause of migraines, which can be set off by large doses of tryamine. Chocolate, however, contains only a very small quantity of tryamine, far less than cheese.
Obesity: Good quality dark chocolate is unlikely to be the cause of obesity because it contains far less sugar than junk chocolate (aka. candy) and, because it is more expensive, is less likely to be eaten to excess.
Acne: American surveys show no correlation between chocolate consumption and acne in teenagers. Likely culprits are hormonal imbalances and a lack of fresh fruit and vegetables in the diet.
Tooth Decay: Chocolate melts in the mouth and is therefore in contact with the teeth for a relatively short time. While the sugar content will contribute to tooth decay, the risk is far less than that associated with sticky candy or toffee, which remain in the mouth longer.
Allergy: Less than 2% of the population have a genuine food allergy, and an allergy to chocolate is extremely rare. It is more likely to be the nuts and milk in chocolate that are the cause, so check the ingredients.
—The Cook’s Encyclopedia of Chocolate